+Open data
-Basic information
Entry | Database: PDB / ID: 6zpg | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Kinesin binding protein (KBP) | |||||||||||||||||||||
Components | KIF-binding protein | |||||||||||||||||||||
Keywords | MOTOR PROTEIN / Kinesin / microtubules / kinesin binding protein / KBP | |||||||||||||||||||||
Function / homology | Function and homology information transport along microtubule / central nervous system projection neuron axonogenesis / mitochondrion transport along microtubule / kinesin binding / neuron projection maintenance / protein sequestering activity / microtubule cytoskeleton organization / in utero embryonic development / cytoskeleton / mitochondrion Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||||||||||||||
Authors | Atherton, J. / Hummel, J.J.A. / Olieric, N. / Locke, J. / Pena, A. / Rosenfeld, S.S. / Steinmetz, M.O. / Hoogenraad, C.C. / Moores, C.A. | |||||||||||||||||||||
Funding support | United Kingdom, Switzerland, United States, 6items
| |||||||||||||||||||||
Citation | Journal: Elife / Year: 2020 Title: The mechanism of kinesin inhibition by kinesin-binding protein. Authors: Joseph Atherton / Jessica Ja Hummel / Natacha Olieric / Julia Locke / Alejandro Peña / Steven S Rosenfeld / Michel O Steinmetz / Casper C Hoogenraad / Carolyn A Moores / Abstract: Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of ...Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of intracellular cargo distribution. Kinesin-binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment, and blocks their cellular function. However, its mechanisms of inhibition and selectivity have been unclear. Here we use cryo-electron microscopy to reveal the structure of KBP and of a KBP-kinesin motor domain complex. KBP is a tetratricopeptide repeat-containing, right-handed α-solenoid that sequesters the kinesin motor domain's tubulin-binding surface, structurally distorting the motor domain and sterically blocking its MT attachment. KBP uses its α-solenoid concave face and edge loops to bind the kinesin motor domain, and selected structure-guided mutations disrupt KBP inhibition of kinesin transport in cells. The KBP-interacting motor domain surface contains motifs exclusively conserved in KBP-interacting kinesins, suggesting a basis for kinesin selectivity. | |||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zpg.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zpg.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 6zpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zpg_validation.pdf.gz | 795.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6zpg_full_validation.pdf.gz | 798.9 KB | Display | |
Data in XML | 6zpg_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 6zpg_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zpg ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zpg | HTTPS FTP |
-Related structure data
Related structure data | 11338MC 6zphC 6zpiC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 71913.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIFBP, KBP, KIAA1279, KIF1BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EK5 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Kinesin binding protein cryo-EM density / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.072 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) Details: Movies were collected with a volta phase plate.Movies were dose weighted. |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
---|---|
EM software | Name: RELION / Category: final Euler assignment |
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258049 / Symmetry type: POINT |